Photocatalysis technology is a promising green route to eliminate antibiotic residues, but current performance still cannot satisfy the practicality. Herein, an EDTA-2Na mediated supramolecular self-assembly strategy was employed to modulate the morphology and microstructure of graphitic carbon nitride (GCN). The obtained EDTA-2Na mediated supermolecule-based GCN (ESGCN) was proved to possess ultrathin flake-like morphology with developed porous structure and Na/O dopants to enhance visible light harvesting. Compared to the pristine GCN and the supermolecule-based GCN (SGCN) without the EDTA-2Na mediation, the ESGCN has more photogenerated charges, decreased charge recombination and accelerated transport/transfer rate, which thus greatly improved photocatalytic activity for degrading tetracycline hydrochloride (TC) and the apparent rate constant is 37.3 and 6.0 times higher than those of the GCN and the SGCN. Additionally, it exhibits excellent universality in degrading various tetracycline antibiotics with a wide pH range and good stability/durability. A possible mechanism of photocatalytic degradation of TC by the ESGCN was elaborated. And the toxicity assessments and mung bean germination experiments also indicate the photocatalytic process can effectively decrease the toxicity and the potential risk of TC to the environment. This work provides a feasible and effective approach to enhance photocatalytic activity of graphitic carbon nitride, which has prominent potentials for elimination of antibiotic residues in environment.